[English] 日本語
Yorodumi- EMDB-5470: Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likel... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5470 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps | |||||||||
Map data | Cryo-EM reconstruction of the structure standard deviation of the fully mature capsid of Nudaurelia capensis omega virus (NwV) | |||||||||
Sample |
| |||||||||
Keywords | time-resolved / single particle reconstruction / virus maturation / protein folding / quasi-equivalence / cryo electron microscopy / Nudaurelia Capensis Omega Virus / maximum likelihood estimation / expectation maximization algorithm / heterogeneous particles / variance map | |||||||||
Biological species | Nudaurelia capensis omega virus | |||||||||
Method | single particle reconstruction / cryo EM | |||||||||
Authors | Wang Q / Matsui T / Domitrovic T / Zheng Y / Doerschuk PC / Johnson JE | |||||||||
Citation | Journal: J Struct Biol / Year: 2013 Title: Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps. Authors: Qiu Wang / Tsutomu Matsui / Tatiana Domitrovic / Yili Zheng / Peter C Doerschuk / John E Johnson / Abstract: CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. ...CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5470.map.gz | 6.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5470-v30.xml emd-5470.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd_5470_1.jpg | 229.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5470 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5470 | HTTPS FTP |
-Validation report
Summary document | emd_5470_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_5470_full_validation.pdf.gz | 77 KB | Display | |
Data in XML | emd_5470_validation.xml.gz | 499 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5470 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5470 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_5470.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM reconstruction of the structure standard deviation of the fully mature capsid of Nudaurelia capensis omega virus (NwV) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.768 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Cryo-EM reconstruction of the structure variance of the fully-mat...
Entire | Name: Cryo-EM reconstruction of the structure variance of the fully-mature capsid of Nudaurelia capensis omega virus (NwV) |
---|---|
Components |
|
-Supramolecule #1000: Cryo-EM reconstruction of the structure variance of the fully-mat...
Supramolecule | Name: Cryo-EM reconstruction of the structure variance of the fully-mature capsid of Nudaurelia capensis omega virus (NwV) type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1 |
---|
-Supramolecule #1: Nudaurelia capensis omega virus
Supramolecule | Name: Nudaurelia capensis omega virus / type: virus / ID: 1 / Name.synonym: NwV (N omega V) / NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: NwV (N omega V) |
---|---|
Host (natural) | Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 400 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK I |
---|
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Date | Feb 13, 2008 |
Image recording | Details: Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline. |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The reconstruction uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. |
---|---|
CTF correction | Details: Each image |
Final reconstruction | Algorithm: OTHER / Number images used: 1200 |